Agricultural Waste Management by Production of Second-Generation Bioethanol from Sugarcane Bagasse Using Indigenous Yeast Strain.

In the wake of rapid industrialization and burgeoning transportation networks, the escalating demand for fossil fuels has accelerated the depletion of finite energy reservoirs, necessitating urgent exploration of sustainable alternatives. To address this, current research is focusing on renewable fuels like second-generation bioethanol from agricultural waste such as sugarcane bagasse. This approach not only circumvents the contentious issue of food-fuel conflicts associated with biofuels but also tackles agricultural waste management. In the present study indigenous yeast strain, Clavispora lusitaniae QG1 (MN592676), was isolated from rotten grapes to ferment xylose sugars present in the hemicellulose content of sugarcane bagasse. To liberate the xylose sugars, dilute acid pretreatment was performed. The highest reducing sugars yield was 1.2% obtained at a temperature of 121 °C for 15 min, a solid-to-liquid ratio of 1:25 (% w/v), and an acid concentration of 1% dilute acid H2SO4 that was significantly higher (P < 0.001) yield obtained under similar conditions at 100 °C for 1 h. The isolated strain was statistically optimized for fermentation process by Plackett-Burman design to achieve the highest ethanol yield. Liberated xylose sugars were completely utilized by Clavispora lusitaniae QG1 (MN592676) and gave 100% ethanol yield. This study optimizes both fermentation process and pretreatment of sugarcane bagasse to maximize bioethanol yield and demonstrates the ability of isolated strain to effectively utilize xylose as a carbon source. The desirable characteristics depicted by strain Clavispora lusitaniae shows its promising utilization in management of industrial waste like sugarcane bagasse by its conversion into renewable biofuels like bioethanol.

In-silico drug design for the novel Karachi-NF001 strain of brain-eating amoeba: Naegleria fowleri.

Naegleria fowleri (N. fowleri) is a free-living thermophilic amoeba of fresh water and soil. The amoeba primarily feeds on bacteria but can be transmitted to humans upon contact with freshwater sources. Furthermore, this brain-eating amoeba enters the human body through the nose and travels to the brain to cause primary amebic meningoencephalitis (PAM). N. fowleri has been reported globally since its discovery in 1961. Recently a new strain of N. fowleri named Karachi-NF001 was found in a patient who had traveled from Riyadh, Saudi Arabia to Karachi in 2019. There were 15 unique genes identified in the genome of the Karachi-NF001 strain compared to all the previously reported strains of N. fowleri worldwide. Six of these genes encode well-known proteins. In this study, we performed in-silico analysis on 5 of these 6 proteins, namely, Rab family small GTPase, NADH dehydrogenase subunit 11, two Glutamine-rich protein 2 proteins (locus tags: 12086 and 12110), and Tigger transposable element-derived protein 1. We conducted homology modeling of these 5 proteins followed by their active site identification. These proteins were subjected to molecular docking against 105 anti-bacterial ligand compounds as potential drugs. Subsequently, the 10 best-docked compounds were determined for each protein and ranked according to the number of interactions and their binding energies. The highest binding energy was recorded for the two Glutamine-rich protein 2 proteins with different locus tags, and results have shown that the protein-inhibitor complex was stable throughout the simulation run. Moreover, future in-vitro studies could validate the findings of our in-silico analysis and identify potential therapeutic drugs against N. fowleri infections.

Vaccinomics to design a multi-epitope-based vaccine against monkeypox virus using surface-associated proteins.

In 2022, the ongoing multi-country outbreak of monkeypox virus-now occurring outside Africa, too is a global health concern. Monkeypox is a zoonotic virus, which causes disease mainly in animals, and then it is transferred to humans. Recently, in the monkeypox epidemic, a large number of human cases emerged while the global health community worked to tackle the outbreak and save lives. Herein, a multi-epitope-based vaccine is designed against monkeypox virus using two surface-associated proteins: MPXVgp002 accession number > YP_010377003.1 and MPXVgp008 accession number > YP_010377007.1 proteins. These proteins were utilized for B- and T-cell epitopes prediction. The epitopes were further screened, and the screen filtered KCKDNEYRSR, RSCNTTHNR, and RTRRETGAS with the antigenicity scores of 0.5279, 0.5604, and 0.7628, respectively. Overall, the epitopes can induce immunity in 99.74% population of the world. Further, GPGPG linkers were used for joining the epitopes and EAAAK linker was used for adjuvant attachment. It has a three-dimensional structure modelled for retaining the structural stability. Three pairs of amino acid residues that were able to make disulfide bonds were chosen: Gly1-Ser82, Cys7-Tyr10, and Phe51-Ile55. Molecular docking of vaccine was done with toll-like receptors, viz., 2, 3, 4, and 8 immune cell receptors. The docking results revealed that the vaccine as potential molecule due to its better binding affinity with toll-like receptors 2, 3, 4 and 8. Top complex in docking in with each receptor was selected based on lowest energy scores- -888.7 kcal/mol (TLR-2), -976.3 kcal/mol (TLR-3), -801.9 kcal/mol (TLR-4), and -955.4 kcal/mol (TLR-4)-were subjected to simulation. The docked complexes were evaluated in 500 ns of MD simulation. Throughout the simulation time, no significant deviation occurred. This confirmed that the vaccine as potential vaccine candidate to interact with immune cell receptors. This interaction is important for the immune system activation. In conclusion, the proposed vaccine construct against monkeypox could induce an effective immune response and speed up the vaccine development process. However, the study is completely based on the computational approach, hence, the experimental validation is required.Communicated by Ramaswamy H. Sarma.

Virtual Screening of Artemisia annua Phytochemicals as Potential Inhibitors of SARS-CoV-2 Main Protease Enzyme.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a human coronaviruses that emerged in China at Wuhan city, Hubei province during December 2019. Subsequently, SARS-CoV-2 has spread worldwide and caused millions of deaths around the globe. Several compounds and vaccines have been proposed to tackle this crisis. Novel recommended in silico approaches have been commonly used to screen for specific SARS-CoV-2 inhibitors of different types. Herein, the phytochemicals of Pakistani medicinal plants (especially Artemisia annua) were virtually screened to identify potential inhibitors of the SARS-CoV-2 main protease enzyme. The X-ray crystal structure of the main protease of SARS-CoV-2 with an N3 inhibitor was obtained from the protein data bank while A. annua phytochemicals were retrieved from different drug databases. The docking technique was carried out to assess the binding efficacy of the retrieved phytochemicals; the docking results revealed that several phytochemicals have potential to inhibit the SARS-CoV-2 main protease enzyme. Among the total docked compounds, the top-10 docked complexes were considered for further study and evaluated for their physiochemical and pharmacokinetic properties. The top-3 docked complexes with the best binding energies were as follows: the top-1 docked complex with a -7 kcal/mol binding energy score, the top-2 docked complex with a -6.9 kcal/mol binding energy score, and the top-3 docked complex with a -6.8 kcal/mol binding energy score. These complexes were subjected to a molecular dynamic simulation analysis for further validation to check the dynamic behavior of the selected top-complexes. During the whole simulation time, no major changes were observed in the docked complexes, which indicated complex stability. Additionally, the free binding energies for the selected docked complexes were also estimated via the MM-GB/PBSA approach, and the results revealed that the total delta energies of MMGBSA were -24.23 kcal/mol, -26.38 kcal/mol, and -25 kcal/mol for top-1, top-2, and top-3, respectively. MMPBSA calculated the delta total energy as -17.23 kcal/mol (top-1 complex), -24.75 kcal/mol (top-2 complex), and -24.86 kcal/mol (top-3 complex). This study explored in silico screened phytochemicals against the main protease of the SARS-CoV-2 virus; however, the findings require an experimentally based study to further validate the obtained results.

NGS-driven molecular diagnosis of heterogeneous hereditary neurological disorders reveals novel and known variants in disease-causing genes.

Hereditary neurological disorders (HNDs) are a clinically and genetically heterogeneous group of disorders. These disorders arise from the impaired function of the central or peripheral nervous system due to aberrant electrical impulses. More than 600 various neurological disorders, exhibiting a wide spectrum of overlapping clinical presentations depending on the organ(s) involved, have been documented. Owing to this clinical heterogeneity, diagnosing these disorders has been a challenge for both clinicians and geneticists and a large number of patients are either misdiagnosed or remain entirely undiagnosed. Contribution of genetics to neurological disorders has been recognized since long; however, the complete picture of the underlying molecular bases are under-explored. The aim of this study was to accurately diagnose 11 unrelated Pakistani families with various HNDs deploying NGS as a first step approach. Using exome sequencing and gene panel sequencing, we successfully identified disease-causing genomic variants these families. We report four novel variants, one each in, ECEL1, NALCN, TBR1 and PIGP in four of the pedigrees. In the rest of the seven families, we found five previously reported pathogenic variants in POGZ, FA2H, PLA2G6 and CYP27A1. Of these, three families segregate a homozygous 18 bp in-frame deletion of FA2H, indicating a likely founder mutation segregating in Pakistani population. Genotyping for this mutation can help low-cost population wide screening in the corresponding regions of the country. Our findings not only expand the existing repertoire of mutational spectrum underlying neurological disorders but will also help in genetic testing of individuals with HNDs in other populations.

'Breast Cancer Resistance Likelihood and Personalized Treatment Through Integrated Multiomics'.

In recent times, enormous progress has been made in improving the diagnosis and therapeutic strategies for breast carcinoma, yet it remains the most prevalent cancer and second highest contributor to cancer-related deaths in women. Breast cancer (BC) affects one in eight females globally. In 2018 alone, 1.4 million cases were identified worldwide in postmenopausal women and 645,000 cases in premenopausal females, and this burden is constantly increasing. This shows that still a lot of efforts are required to discover therapeutic remedies for this disease. One of the major clinical complications associated with the treatment of breast carcinoma is the development of therapeutic resistance. Multidrug resistance (MDR) and consequent relapse on therapy are prevalent issues related to breast carcinoma; it is due to our incomplete understanding of the molecular mechanisms of breast carcinoma disease. Therefore, elucidating the molecular mechanisms involved in drug resistance is critical. For management of breast carcinoma, the treatment decision not only depends on the assessment of prognosis factors but also on the evaluation of pathological and clinical factors. Integrated data assessments of these multiple factors of breast carcinoma through multiomics can provide significant insight and hope for making therapeutic decisions. This omics approach is particularly helpful since it identifies the biomarkers of disease progression and treatment progress by collective characterization and quantification of pools of biological molecules within and among the cancerous cells. The scrupulous understanding of cancer and its treatment at the molecular level led to the concept of a personalized approach, which is one of the most significant advancements in modern oncology. Likewise, there are certain genetic and non-genetic tests available for BC which can help in personalized therapy. Genetically inherited risks can be screened for personal predisposition to BC, and genetic changes or variations (mutations) can also be identified to decide on the best treatment. Ultimately, further understanding of BC at the molecular level (multiomics) will define more precise choices in personalized medicine. In this review, we have summarized therapeutic resistance associated with BC and the techniques used for its management.

Binge eating disorder during COVID-19.

With the onset of coronavirus disease in December 2019, the normal routine and lifestyle of the humans has adversely affected all over the world. This change in lifestyle not only increased the level of stress and anxiety, but also badly modified the eating habits during the lockdown period. This increased the rate of binge eating disorder in people who were already immune-compromised. This rapid communication aims to develop awareness among people to stay calm during this pandemic and eat healthy.

Climate beast: a potential threat for repercussions of disease status in Pakistan.

Pakistan is amongst the developing countries, which have been strongly affected by several emerging and re-emerging disease outbreaks as a consequence of climate change. Various studies have clearly demonstrated the impact of climate change on human health in Pakistan. This has increased the rate of morbidity and mortality, related not only to vector-borne, water-borne and food-borne diseases but has also contributed to the prevalence of neurological, cardiovascular and respiratory disorders. It is therefore important to take adequate measurements for water management and improve sanitary conditions especially in case of natural disasters. In order to effectively control the emerging and re-emerging infections in the country, an early, more Rigorous response is required, by the national health department, to monitor and evaluate the spread of infections in future. Therefore, precise planning and management strategies should be defined in order to circumvent the damage caused by the natural disasters associated with climate changes. This mini-review gives an overview about the public health issues associated with environmental change with special reference to Pakistan. This will provide a baseline for policymakers to develop public health surveillance programs in Pakistan.

Climate engineering: a strategic approach to combat environmental potential risks associated with Pak-China Economic corridor (CPEC) Development.

China-Pak Economic Corridor (CPEC) has become a future economic potential for both countries. It will serve as a gateway to share trade and other industrial benefits with each other. On one hand it's a blessing for both countries, the other way it is offering a potential threat to the environment i.e. due to wide construction of roads the major effect is threatening biodiversity and environmental sustainability. It will cause deforestation, floods, glacier melting, climate change, and global warming. "Climate engineering" is the newly emerging concept to resolve the problems related to the environment and biodiversity. Under the umbrella of concept "Climate engineering" we proposed attractive and environmentally friendly solutions that are helpful to mitigate the impact of anthropogenic activities on the environment of both countries. These proposed strategies include installation of CO2 scrubbers, construction of Algal ponds, and development of research stations across the roads and by introducing the concept of carbon canopy. It will also help the legislators and policymakers of both countries to incorporate these solutions for sustainable development on each side.

A full-scale comparison of two hybrid constructed wetlands treating domestic wastewater in Pakistan.

Objective of the current work was to monitor the year-round response of full-scale hybrid constructed-wetlands (CWs) treating domestic wastewater under variable continuous flow. Two systems were evaluated: system-I consisted of an anaerobic baffled reactor (ABR) followed by a saturated vertical subsurface-flow (VSSF) CW and a free-water-surface (FWS) CW as a tertiary treatment; system-II consisted of an ABR followed by a horizontal subsurface-flow (HSSF) CW and FWS. Maximum reduction of 80 and 78%, 81 and 82%, 63 and 69%, 79 and 89% for chemical oxygen demand (COD), biological oxygen demand (BOD), total kjeldahl nitrogen (TKN) and total suspended solids (TSS) was achieved in Systems I and II respectively. There was also effective removal (94% and 93%) of the bacterial population in both systems while more than 94% of pathogenic microorganisms were removed. Data from both systems were further used to compute the first-order rate constants for the k-C* model commonly used in CW design. The treatment performance was confirmed to follow a first-order reaction rate, in which the k20 values of chemical oxygen demand (COD), biological oxygen demand (BOD), total kjeldahl nitrogen (TKN), total phosphorus (TP) and total suspended solids were calculated as 165, 117, 133, 7.5 and 78 m yr-1 respectively for VSSF and 226, 134, 199, 22 and 73 m yr-1 respectively for HSSF. A positive correlation with temperature was discovered for all parameters in both systems.

Psychological morbidity in children 18 months after Kashmir Earthquake of 2005.

A severe earthquake occurred in Kashmir in 2005. The epicentre was close to Muzzafarabad. We collected data on over 1,100 children 18 months after the earthquake to look at symptoms of PTSD and behavioural and emotional problems using well established questionnaires. We found that 64.8% of children had significant symptoms of PTSD. Girls were more likely to suffer from these symptoms. The proportion of children suffering from emotional and behaviour difficulties was 34.6%. This percentage was not different from other studies of children from Pakistan within areas which were not affected by the earthquake. The rate of emotional symptoms was higher in girls while hyperactivity was more frequent in boys. This pattern is similar to other studies from across the world.

Paralytic ileus associated with use of diltiazem.

PURPOSE: A case of paralytic ileus in a patient receiving oral diltiazem therapy for atrial fibrillation is reported. SUMMARY: A 64-year-old man with a history of multiple serious comorbidities, poly-pharmacy, and a recent hospital stay for acute cardiac problems was readmitted to the hospital for gastrointestinal (GI) bleeding. On day 2 of the readmission, he suffered a myocardial infarction complicated by atrial fibrillation with a rapid ventricular response. After initial treatment with oral metoprolol for ventricular rate control was discontinued (due to ineffective rate control and patient complaints of respiratory symptoms), oral diltiazem hydrochloride therapy (30 mg every six hours) was initiated on day 7; the dose was adjusted to a maximum of 120 mg every six hours on day 10. On day 12, the patient complained of nausea, abdominal pain and tenderness, and infrequent bowel movements; imaging studies on day 13 indicated paralytic ileus. Pursuant to a surgical consultation, a nasogastric tube was inserted and nothing was given by mouth except medications. After initial improvement of the GI symptoms, the feeding tube was removed; however, the symptoms worsened over the next two to three days, requiring reinsertion of the tube on day 16. On day 18, after other potential causes of ileus were ruled out, diltiazem therapy was withdrawn. The man experienced rapid symptomatic improvement, with no further GI symptoms, and was discharged four days later. CONCLUSION: A 64-year-old man receiving high-dose diltiazem to treat atrial fibrillation developed paralytic ileus, which quickly resolved after the medication was discontinued.